Resources

BRCA

But keep in mind that it’s a mutation in BRCA that’s associated with an increased risk of cancer. These data are not comparing normal and mutation.

Looking for the relationship between the BRCA gene and cancer.

Paul Overvoorde provided a file from the NCI site. [NEED MORE DETAILS]. It gives gene expression levels in 60 subjects.

fileName <- "/Users/kaplan/Downloads/filesandlinks/nci60_RNA__Agilent_mRNA_log2.txt/nci60_RNA__Agilent_mRNA_log2.txt"
geneExpress <- read.table( fileName, head=TRUE )
geneNames <- as.character(geneExpress$Probe)

Find the ones with a name indicating BRC

keepers <- filter(geneExpress, grepl("BRC", as.character(Probe)))
nrow(keepers)
## [1] 4

There are 4 such genes.

Transform from a wide format (where each column is a patient) to a narrow format (where columns are cell-line, probe, measurement).

express <- melt(keepers,variable='Cell.Line.Name',value.name='expression')
## Using Experiment, Name, symbol, Probe, Name.1 as id variables
allgenes <- melt(geneExpress,variable='Cell.Line.Name',value.name='expression' )
## Using Experiment, Name, symbol, Probe, Name.1 as id variables

The information about the cell lines:

cellLineFile <- "/Users/kaplan/KaplanFiles/DCF-2014/CaseStudies/NCI-gene/nci60_cellline_metadata.csv"
cellLineData <- read.csv( cellLineFile, head=TRUE)
# There are different punctuations in the Cell.Line.Names for express and cellLineData.
cellLineData <- mutate(cellLineData, Cell.Line.Name=sub(":",'.',Cell.Line.Name))
both <- inner_join(express , cellLineData)
## Joining by: "Cell.Line.Name"
bothall <- inner_join(allgenes, cellLineData)
## Joining by: "Cell.Line.Name"

Construct the table for BRCA1

origs <- c('BRCA1','DTX3L',"BID","CALU","BFAR", "NONO")
top100 <- c('ACTG2' , 'SULF1' , 'COL3A1' , 'IGFBP5' , 'SLC24A3' , 'COL1A2' , 'LUM' , 'SPARC' , 'POSTN' , 'CXCL1' , 'A_23_P37685' , 'MGC16121' , 'UCHL1' , 'A_23_P203120' , 'ALDH2' , 'DCN' , 'DPYSL3' , 'CPXM2' , 'WISP1' , 'CDKN2A' , 'FEZ1' , 'CBS' , 'A_24_P372189' , 'CDCP1' , 'C10orf58' , 'CNN1' , 'A_32_P74409' , 'SYNPO2' , 'CDCP1' , 'WNT5A' , 'A_23_P305292' , 'KIAA0746' , 'COL1A1' , 'CDH11' , 'A_24_P299474' , 'GPR110' , 'A_23_P36226' , 'A_32_P214011' , 'A_23_P217901' , 'SPOCK1' , 'ACTA2' , 'KRT19' , 'A_24_P563966' , 'KRT17' , 'CXCL12' , 'KCNG1' , 'HSPB2' , 'VCX2' , 'FAP' , 'MRVI1' , 'TSHZ3' , 'ADAMTS4' , 'COL3A1' , 'OLFML3' , 'IFITM1' , 'RIMS2' , 'C19orf33' , 'BST2' , 'DPYSL3' , 'C11orf41' , 'VCX' , 'C5orf23' , 'CSTA' , 'ROBO1' , 'FOXD1' , 'IGFBP5' , 'CD248' , 'MX1' , 'ZNF469' , 'PLAC8' , 'ADFP' , 'APCDD1L' , 'CDH13' , 'CTHRC1' , 'SAA1' , 'A_32_P55241' , 'TMEM98' , 'COX7A1' , 'CST6' , 'A_23_P206741' , 'FAM101B' , 'A_32_P96752' , 'FKBP10' , 'BDKRB1' , 'A_24_P691826' , 'A_24_P887857' , 'VCX3A' , 'PCSK9' , 'ADAMTS5' , 'CTAG1A' , 'SIPA1L2' , 'A_24_P828496' , 'ROBO3' , 'G0S2' , 'KCNMA1' , 'ITGA8' , 'PLAC8' , 'PRAME' , 'PTGIS' , 'MAGEA2B' )
probeSet <- c(origs, top100)
res <- list()
for (probe in probeSet) {
  filter(bothall, Probe==probe) %>% 
  group_by(tissue.of.origin) %>% 
  summarize(ave=mean(expression),stderr=sd(expression)/sqrt(n())) -> tmp
  tmp$tissue.of.origin <- with(tmp,reorder(tissue.of.origin,-ave))
  res[[probe]] <- tmp
}
Fres <- data.frame( probe=character(length(probeSet)), F=NA, p=NA,
                    stringsAsFactors=FALSE)
for (probe in probeSet) {
  P1 <- ggplot(data=res[[probe]], aes(x=tissue.of.origin,y=ave,color=tissue.of.origin)) 
  P2 <- P1 + 
    geom_bar(stat='identity',position='dodge',alpha=0.2,color='gray') +
    geom_errorbar(aes(ymax=ave+2*stderr,ymin=ave-2*stderr),
                  width=0.2,position=position_dodge(width=0.8))
  raw <- filter(bothall, Probe==probe)
  P3 <- P2 + geom_point(data=raw,
                        position=position_jitter(width=0.15),
                        aes(y=expression),alpha=.5)
  print(P3 + ggtitle(probe) + xlab('Tissue type') +
          ylab('Expression level (log2)') +
          theme_tufte() + coord_flip())
  tmp <- anova(lm(expression ~ tissue.of.origin, data=raw))
  print(tmp)
  Fres[which(probe == probeSet),] <- list(probe=probe, F=tmp[1,4], p=tmp[1,5] )
  }

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8   10.8    1.35     4.1 0.00079 ***
## Residuals        51   16.8    0.33                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin   8     34    4.25    3.41 0.0015 **
## Residuals        111    138    1.24                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin   8     20    2.54    0.78   0.62
## Residuals        111    363    3.27

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8   37.5    4.68    7.03 3.2e-06 ***
## Residuals        51   34.0    0.67                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin   8   28.4    3.55    1.87  0.072 .
## Residuals        111  211.0    1.90                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin   8    4.3   0.538    1.06    0.4
## Residuals        111   56.4   0.508

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    155   19.32     2.9 0.0096 **
## Residuals        51    340    6.66                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    191   23.87    3.08 0.0065 **
## Residuals        51    395    7.74                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    303    37.9    6.27 4.2e-07 ***
## Residuals        171   1035     6.0                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8    649    81.1    17.1 <2e-16 ***
## Residuals        171    812     4.7                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    106   13.24    4.31 0.00015 ***
## Residuals        111    341    3.07                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8    632    79.0    11.4  1e-11 ***
## Residuals        111    767     6.9                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8    129   16.06    1.94  0.074 .
## Residuals        51    422    8.28                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8   1060   132.4    11.6 3.5e-09 ***
## Residuals        51    584    11.5                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8   61.9    7.74    1.75   0.11
## Residuals        51  225.0    4.41

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    562    70.3    5.39 6.2e-05 ***
## Residuals        51    665    13.0                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8     43    5.42    0.76   0.63
## Residuals        51    361    7.09

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    117   14.65    3.85 0.0013 **
## Residuals        51    194    3.81                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8   1214   151.7    7.26 2.2e-06 ***
## Residuals        51   1066    20.9                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    330    41.3    3.17 0.0054 **
## Residuals        51    664    13.0                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    575    71.8    7.39 7.5e-08 ***
## Residuals        111   1079     9.7                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8   30.8    3.84    1.33   0.25
## Residuals        51  146.9    2.88

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    452    56.4    5.25 1.4e-05 ***
## Residuals        111   1193    10.8                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8   30.3    3.79    1.06   0.41
## Residuals        51  182.4    3.58

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8   85.4   10.67    4.05  3e-04 ***
## Residuals        111  292.4    2.63                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin   8    368    46.0     2.6  0.012 *
## Residuals        111   1964    17.7                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8    340    42.5    7.96  2e-08 ***
## Residuals        111    593     5.3                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin   8    233   29.07    3.19 0.0027 **
## Residuals        111   1013    9.13                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8   76.7    9.59    2.84  0.011 *
## Residuals        51  172.1    3.37                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8    964   120.5    15.9 <2e-16 ***
## Residuals        171   1294     7.6                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    176   22.04    3.25 0.0046 **
## Residuals        51    346    6.78                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    235   29.41    4.15 0.00071 ***
## Residuals        51    361    7.08                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin  8    241   30.11    3.98  0.001 ***
## Residuals        51    386    7.56                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin   8   34.8    4.35    1.73  0.099 .
## Residuals        111  279.1    2.51                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8    964   120.5    15.9 <2e-16 ***
## Residuals        171   1294     7.6                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    266    33.3    4.29 0.00054 ***
## Residuals        51    396     7.8                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8   33.2    4.15    1.32   0.25
## Residuals        51  159.9    3.14

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    339    42.4    7.64 1.2e-06 ***
## Residuals        51    283     5.6                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    285    35.7    4.54 0.00033 ***
## Residuals        51    401     7.9                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    287    35.9    3.79 0.0015 **
## Residuals        51    483     9.5                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    480    60.0    6.11 1.6e-05 ***
## Residuals        51    501     9.8                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    196   24.52    4.67 3.5e-05 ***
## Residuals        171    899    5.25                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8   44.6    5.57    2.29  0.035 *
## Residuals        51  124.2    2.44                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    148   18.55    3.45  0.003 **
## Residuals        51    274    5.38                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8    279    34.9    2.78  0.012 *
## Residuals        51    640    12.5                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    396    49.4    5.65 3.8e-05 ***
## Residuals        51    446     8.7                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8    101   12.60    1.69   0.12
## Residuals        51    381    7.47

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8   1151   143.8    11.6 3.5e-09 ***
## Residuals        51    635    12.4                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8   47.1    5.89    2.87   0.01 *
## Residuals        51  104.7    2.05                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8   80.5   10.06       2  0.065 .
## Residuals        51  256.6    5.03                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    327    40.9    8.31 1.7e-09 ***
## Residuals        171    841     4.9                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    192   23.95    5.45 8.4e-06 ***
## Residuals        111    488    4.39                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8    189    23.7    2.08  0.055 .
## Residuals        51    580    11.4                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin   8    102   12.80    2.41   0.02 *
## Residuals        111    591    5.32                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    302    37.7    4.66 0.00026 ***
## Residuals        51    413     8.1                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8     27    3.38    1.44    0.2
## Residuals        51    120    2.35

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    265    33.1    5.02 0.00013 ***
## Residuals        51    337     6.6                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    137   17.13    5.08 2.1e-05 ***
## Residuals        111    374    3.37                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    303    37.9    6.27 4.2e-07 ***
## Residuals        171   1035     6.0                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin   8     82   10.23    2.21  0.031 *
## Residuals        111    513    4.62                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    292    36.5    3.21  0.005 **
## Residuals        51    580    11.4                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin   8     59    7.31    1.62   0.12
## Residuals        171    773    4.52

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8   1699   212.4    73.1 <2e-16 ***
## Residuals        111    322     2.9                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8    193    24.1    2.02  0.063 .
## Residuals        51    610    12.0                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    452    56.4    5.25 1.4e-05 ***
## Residuals        111   1193    10.8                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin  8    355    44.4    6.78  5e-06 ***
## Residuals        51    334     6.5                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8     89   11.16    1.29   0.27
## Residuals        51    440    8.62

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    234   29.30    4.34 0.00049 ***
## Residuals        51    344    6.75                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin   8     44    5.55    1.05    0.4
## Residuals        111    587    5.29

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8    342    42.8     6.3  1e-06 ***
## Residuals        111    753     6.8                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin   8    133   16.60    2.67   0.01 *
## Residuals        111    690    6.22                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8    649    81.1    17.1 <2e-16 ***
## Residuals        171    812     4.7                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8   12.4    1.55    0.83   0.58
## Residuals        51   95.2    1.87

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8     41    5.07    0.49   0.86
## Residuals        51    530   10.40

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    209   26.18    4.07 0.00084 ***
## Residuals        51    328    6.43                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    467    58.4     5.4 9.4e-06 ***
## Residuals        111   1199    10.8                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    201   25.16    4.36 0.00047 ***
## Residuals        51    294    5.77                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8    112   13.99    2.23   0.04 *
## Residuals        51    320    6.27                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8    176    22.0    1.93  0.075 .
## Residuals        51    581    11.4                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    277    34.7    3.12 0.0061 **
## Residuals        51    567    11.1                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    194   24.27    3.51 0.0027 **
## Residuals        51    353    6.93                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    183   22.91    3.47 0.0029 **
## Residuals        51    337    6.61                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    425    53.1    6.49 6.5e-07 ***
## Residuals        111    909     8.2                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8   97.4   12.17    4.61 0.00028 ***
## Residuals        51  134.6    2.64                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    379    47.3     6.6 6.9e-06 ***
## Residuals        51    366     7.2                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8   52.3    6.53    2.34  0.032 *
## Residuals        51  142.6    2.80                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8    312    39.0    4.74  5e-05 ***
## Residuals        111    913     8.2                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8   24.1    3.01    0.59   0.78
## Residuals        51  259.3    5.08

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin  8    306    38.2    7.87  8e-07 ***
## Residuals        51    248     4.9                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    300    37.5    3.99 0.00034 ***
## Residuals        111   1042     9.4                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin  8    201   25.10    4.57  3e-04 ***
## Residuals        51    280    5.49                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8     80   10.00    2.44  0.025 *
## Residuals        51    209    4.09                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8     75    9.40     1.3   0.27
## Residuals        51    369    7.24

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)   
## tissue.of.origin  8    299    37.4    3.23 0.0048 **
## Residuals        51    590    11.6                  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

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## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    263    32.8     4.5 0.00035 ***
## Residuals        51    372     7.3                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8    161    20.1    1.42   0.21
## Residuals        51    723    14.2

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8     36    4.51    0.72   0.67
## Residuals        51    320    6.27

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8   95.9   11.99    2.48  0.023 *
## Residuals        51  246.1    4.83                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin   8     55    6.87    1.98  0.052 .
## Residuals        171    594    3.47                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)  
## tissue.of.origin  8    329    41.1     2.3  0.035 *
## Residuals        51    911    17.9                 
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value Pr(>F)    
## tissue.of.origin   8    777    97.1    21.3 <2e-16 ***
## Residuals        291   1325     4.6                   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value Pr(>F)
## tissue.of.origin  8    7.3   0.917    0.68    0.7
## Residuals        51   68.3   1.339

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    467    58.4     5.4 9.4e-06 ***
## Residuals        111   1199    10.8                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    992     124    12.4 1.3e-12 ***
## Residuals        111   1107      10                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                   Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin   8    235    29.4    6.26 1.1e-06 ***
## Residuals        111    522     4.7                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

plot of chunk unnamed-chunk-8

## Analysis of Variance Table
## 
## Response: expression
##                  Df Sum Sq Mean Sq F value  Pr(>F)    
## tissue.of.origin  8    610    76.2    5.16 9.7e-05 ***
## Residuals        51    754    14.8                    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Fres
##            probe       F         p
## 1          BRCA1  4.0983 7.890e-04
## 2          DTX3L  3.4102 1.533e-03
## 3            BID  0.7771 6.236e-01
## 4           CALU  7.0343 3.231e-06
## 5           BFAR  1.8667 7.232e-02
## 6           NONO  1.0584 3.975e-01
## 7          ACTG2  2.8988 9.650e-03
## 8          SULF1  3.0825 6.532e-03
## 9         COL3A1  6.2655 4.179e-07
## 10        IGFBP5 17.0880 1.569e-18
## 11       SLC24A3  4.3145 1.499e-04
## 12        COL1A2 11.4289 1.024e-11
## 13           LUM  1.9402 7.385e-02
## 14         SPARC 11.5583 3.469e-09
## 15         POSTN  1.7535 1.086e-01
## 16         CXCL1  5.3910 6.234e-05
## 17   A_23_P37685  0.7649 6.348e-01
## 18      MGC16121  3.8483 1.316e-03
## 19         UCHL1  7.2614 2.194e-06
## 20  A_23_P203120  3.1743 5.378e-03
## 21         ALDH2  7.3890 7.536e-08
## 22           DCN  1.3348 2.480e-01
## 23        DPYSL3  5.2497 1.393e-05
## 24         CPXM2  1.0587 4.063e-01
## 25         WISP1  4.0498 2.957e-04
## 26        CDKN2A  2.5982 1.215e-02
## 27          FEZ1  7.9552 2.007e-08
## 28           CBS  3.1855 2.730e-03
## 29  A_24_P372189  2.8430 1.087e-02
## 30         CDCP1 15.9243 1.931e-17
## 31      C10orf58  3.2515 4.569e-03
## 32          CNN1  4.1514 7.083e-04
## 33   A_32_P74409  3.9832 9.978e-04
## 34        SYNPO2  1.7293 9.930e-02
## 35         CDCP1 15.9243 1.931e-17
## 36         WNT5A  4.2884 5.370e-04
## 37  A_23_P305292  1.3233 2.534e-01
## 38      KIAA0746  7.6441 1.157e-06
## 39        COL1A1  4.5350 3.279e-04
## 40         CDH11  3.7883 1.489e-03
## 41  A_24_P299474  6.1116 1.642e-05
## 42        GPR110  4.6671 3.509e-05
## 43   A_23_P36226  2.2880 3.548e-02
## 44  A_32_P214011  3.4505 3.007e-03
## 45  A_23_P217901  2.7832 1.235e-02
## 46        SPOCK1  5.6526 3.815e-05
## 47         ACTA2  1.6859 1.246e-01
## 48         KRT19 11.5566 3.477e-09
## 49  A_24_P563966  2.8710 1.024e-02
## 50         KRT17  1.9999 6.518e-02
## 51        CXCL12  8.3059 1.730e-09
## 52         KCNG1  5.4515 8.395e-06
## 53         HSPB2  2.0831 5.474e-02
## 54          VCX2  2.4060 1.964e-02
## 55           FAP  4.6587 2.567e-04
## 56         MRVI1  1.4406 2.027e-01
## 57         TSHZ3  5.0165 1.276e-04
## 58       ADAMTS4  5.0838 2.116e-05
## 59        COL3A1  6.2655 4.179e-07
## 60        OLFML3  2.2144 3.148e-02
## 61        IFITM1  3.2112 4.975e-03
## 62         RIMS2  1.6186 1.227e-01
## 63      C19orf33 73.1020 1.086e-40
## 64          BST2  2.0157 6.306e-02
## 65        DPYSL3  5.2497 1.393e-05
## 66      C11orf41  6.7831 4.985e-06
## 67           VCX  1.2948 2.673e-01
## 68       C5orf23  4.3385 4.855e-04
## 69          CSTA  1.0498 4.037e-01
## 70         ROBO1  6.3004 1.029e-06
## 71         FOXD1  2.6687 1.018e-02
## 72        IGFBP5 17.0880 1.569e-18
## 73         CD248  0.8299 5.805e-01
## 74           MX1  0.4880 8.591e-01
## 75        ZNF469  4.0699 8.359e-04
## 76         PLAC8  5.4045 9.444e-06
## 77          ADFP  4.3579 4.670e-04
## 78       APCDD1L  2.2305 4.009e-02
## 79         CDH13  1.9299 7.544e-02
## 80        CTHRC1  3.1187 6.050e-03
## 81          SAA1  3.5052 2.682e-03
## 82   A_32_P55241  3.4672 2.904e-03
## 83        TMEM98  6.4920 6.451e-07
## 84        COX7A1  4.6121 2.814e-04
## 85          CST6  6.6011 6.853e-06
## 86  A_23_P206741  2.3369 3.197e-02
## 87       FAM101B  4.7423 5.028e-05
## 88   A_32_P96752  0.5924 7.796e-01
## 89        FKBP10  7.8690 7.999e-07
## 90        BDKRB1  3.9903 3.445e-04
## 91  A_24_P691826  4.5749 3.029e-04
## 92  A_24_P887857  2.4437 2.547e-02
## 93         VCX3A  1.2989 2.653e-01
## 94         PCSK9  3.2326 4.755e-03
## 95       ADAMTS5  4.5006 3.511e-04
## 96        CTAG1A  1.4210 2.105e-01
## 97       SIPA1L2  0.7184 6.743e-01
## 98  A_24_P828496  2.4844 2.335e-02
## 99         ROBO3  1.9795 5.168e-02
## 100         G0S2  2.2997 3.461e-02
## 101       KCNMA1 21.3184 1.992e-25
## 102        ITGA8  0.6849 7.027e-01
## 103        PLAC8  5.4045 9.444e-06
## 104        PRAME 12.4337 1.345e-12
## 105        PTGIS  6.2596 1.137e-06
## 106      MAGEA2B  5.1593 9.692e-05